Passivation with elements other than Hydrogen

[bobslinger]

Hello all,

I am trying to passivate a spherical Carbon structure with elements other than Hydrogen (e.g. N, O, P).
Since such a function seems non existent in VirtualNanoLab (why?!), and I only have the "CustomPassivator" of the CoordinateTools at my disposal, I tried the following workaround: change the bond distance of CustomPassivator for Hydrogen to the desired values and after the passivation, replace H with the element I desire. By doing this I encountered a problem, namely that depending on the bond distance I select, the structure will be passivated by a different number of Hydrogen atoms, so that I have a varying number of passivation Atoms for N, O, P, when I would like to have the same number of passivations as I have when I use Hydrogen (with bond distance 1.09 Ang).
So my questions are:
Is there a passivation function, that I have somehow not found, with which I can passivate very easily using other elemens? If there is not, why is that not a tool somewhere in VNL (it seems to me that this might be something one commonly wants to do)?
Is there an option to change the bond distance (pairwise) by (for example) using the "Select by bond distance" tool?
Is there an option to adjust the bond distance to a desired value when changing Hydrogen elements (after I passivated my structure with it) to another element?

Currently, what I have to do, is to passivate my structure with hydrogen and then INDIVIDUALLY replacing Hydrogen with the desired element and then change the distance value to the corresponding bonded Atom by using the Z-Matrix to ensure it actually is the same number of passivations. That, I have to do around 800 times.

Please, if there is anything remotely related to solving or simplifying this problem, give me a hint.

[Nordland]

One trick that could bring you a part of the way, is that if you use the Custom Passivator, all atoms that you add will get a tag, and if you then use the selection tool (Tag) you can select all of thoses atoms with a single click and replace them with your choice of element.

[bobslinger]

One trick that could bring you a part of the way, is that if you use the Custom Passivator, all atoms that you add will get a tag, and if you then use the selection tool (Tag) you can select all of thoses atoms with a single click and replace them with your choice of element.

Yes, I did this. Maybe I did not explain clear enough what the problem is:
If:::1. I use the CustomPassivator to passivate with Hydrogen with bond distance 1.09Ang and then change Hydrogen to something else ---> Problem: the bond distance does not change automatically to "something else".
If:::2. I use the CustomPassivator to passivate with Hydrogen with bond distance of the other elements I want to use (e.g. 1.47Ang for Nitrogen Passivation) and then I change Hydrogen to something else (e.g. Nitrogen) ---> Problem: CustomPassivator passivates with A DIFFERENT NUMBER of Hydrogen Atoms, if change the Bond distance from 1.09Ang to "something else".
If:::3. I use the CustomPassivator to passivate with Hydrogen with bond distance 1.09Ang and then change Hydrogen to something else, then select a  Carbon Atom and a Hydrogen Atom and change their distance to "something else" (e.g. 1.47Ang for Nitrogen Passivation) by using the Z-Matrix and then change Hydrogen to "something else" (e.g. Nitrogen for Nitrogen Passivation). ---> Problem: If the system is large enough (it is), I will be using my Mouse and Keyboard to select Atoms and change entries in the Z-Matrix until the end of time.

[Anders Blom]

2 should work, but you also need to make sure you control the hybridization.

[bobslinger]

2 should work, but you also need to make sure you control the hybridization.

It does not. That is why I am writing in this forum.

[Anders Blom]

2 should work, but you also need to make sure you control the hybridization.

It does not. That is why I am writing in this forum.

Ok, but then we need more details, like the structure used, and the result you are getting. Else we're just operating blindly. If your structure is secret you can share it via support@quantumwise.com instead.

[Trung Phuc]

"If:::3. I use the CustomPassivator to passivate with Hydrogen with bond distance 1.09Ang and then change Hydrogen to something else, then select a  Carbon Atom and a Hydrogen Atom and change their distance to "something else" (e.g. 1.47Ang for Nitrogen Passivation) by using the Z-Matrix and then change Hydrogen to "something else" (e.g. Nitrogen for Nitrogen Passivation). ---> Problem: If the system is large enough (it is), I will be using my Mouse and Keyboard to select Atoms and change entries in the Z-Matrix until the end of time."
Personally, I think the third method is more convenient when you just do this for one unit cell. After optimizing, you will repeat this optimized unit cell to have your whole structure.